all of the shell tools now deal properly with resource forks. if they still have to, that is: ...
Well, that depends how you're defining "shell tools". :-)
It's still very easy to accidentally zap resource forks if you're not careful manipulating files with many Unix commands. Any sort of stdout redirection can be troublesome, e.g. substitutions/replacements using traditional Unix commands like awk, sed, etc. since none of them (or any shells!) are resource fork-aware. Using language commands like perl, python, ruby (invoked directly or indirectly) can easily clobber resource forks. The BOMArchive GUI tool preserve resource forks but zip/unzip commands don't. Pick your poison.